Systems and methods for detecting genetic alterations

Abstract

Disclosed are systems and methods for detecting genetic alterations comprising androgen receptor gene splice variants (AR-Vs), mutations, indel, copy number changes, fusion and combination thereof, in a biofluid sample from the patient. The systems and methods are similarly applicable to the detection of gene alterations comprising gene splicing variants, mutations, indel, copy number changes, fusion and combination thereof of other genes of interest. The streamlined methods improve the consistency and simplicity of non-invasive detections of biomarkers.

What is claimed is: 
     
         1 . A method for detecting castration resistant prostate cancer in a subject, comprising:
 (a) assaying a biofluid sample obtained or derived from the subject to determine a presence or an absence of an androgen receptor gene splice variant (AR-V) or AR gene mutation in the biofluid sample; and   (b) detecting castration resistant prostate cancer in the subject, based at least in part on the presence or the absence of the AR-V or AR gene mutation in the biofluid sample.   
     
     
         2 . The method of  claim 1 , wherein the biofluid sample is selected from the group consisting of a blood sample, a plasma sample, a serum sample, a urine sample, a sputum sample, a spinal fluid sample, a cerebrospinal fluid sample, a pleural fluid sample, a nipple aspirate sample, a lymph fluid sample, a fluid sample of the respiratory, intestinal, or genitourinary tracts, a tear sample, a saliva sample, a breast milk sample, a fluid sample from a lymphatic system, a semen sample, an intra-organ system fluid sample, an ascitic fluid sample, a tumor cyst fluid sample, an amniotic fluid sample, and a combination thereof. 
     
     
         3 . The method of  claim 2 , wherein the biofluid sample is the plasma sample. 
     
     
         4 . The method of  claim 2 , wherein the biofluid sample is the urine sample. 
     
     
         5 . The method of  claim 1 , wherein the biofluid sample is a cell-free sample. 
     
     
         6 . The method of  claim 5 , wherein (a) further comprises assaying cell-free DNA molecules or cell-free RNA molecules, and wherein (b) further comprises detecting the castration resistant prostate cancer in the subject, based at least in part on the presence or the absence of the AR-V or the AR gene mutation in the cell-free DNA molecules or cell-free RNA molecules. 
     
     
         7 . The method of  claim 6 , wherein (a) further comprises assaying cell-free DNA molecules and cell-free RNA molecules, and wherein (b) further comprises detecting the castration resistant prostate cancer in the subject, based at least in part on the presence or the absence of the AR-V or the AR gene mutation in the cell-free DNA molecules and the cell-free RNA molecules. 
     
     
         8 . The method of  claim 1 , wherein (a) further comprises determining the presence or the absence of the AR-V in the biofluid sample, and wherein (b) further comprises detecting the castration resistant prostate cancer in the subject, based at least in part on the presence or the absence of the AR-V in the biofluid sample. 
     
     
         9 . The method of  claim 8 , wherein the AR-V is selected from the group consisting of AR-V1, AR-V2, AR-V7, AR-V9, and AR-V567es. 
     
     
         10 . The method of  claim 1 , wherein (a) further comprises determining the presence or the absence of the AR gene mutation in the biofluid sample, and wherein (b) further comprises detecting the castration resistant prostate cancer in the subject, based at least in part on the presence or the absence of the AR gene mutation in the biofluid sample. 
     
     
         11 . The method of  claim 10 , wherein the AR gene mutation is selected from the group consisting of AR-FL, AR-T878A, and AR-F876L. 
     
     
         12 . The method of  claim 1 , wherein (a) further comprises extracting ribonucleic acid (RNA) molecules from the biofluid sample, and reverse transcribing the extracted RNA molecules to produce complementary deoxyribonucleic acid (DNA) molecules. 
     
     
         13 . The method of  claim 1 , wherein (a) further comprises extracting both DNA molecules and RNA molecules from the biofluid sample simultaneously, and reverse transcribing the extracted RNA molecules to produce complementary DNA molecules. 
     
     
         14 . The method of  claim 13 , further comprising sequencing the complementary DNA molecules to produce sequence reads, and analyzing the sequence reads to determine the presence or the absence of the AR-V or the AR gene mutation in the biofluid sample. 
     
     
         15 . The method of  claim 13 , further comprising analyzing the complementary DNA molecules using polymerase chain reaction. 
     
     
         16 . The method of  claim 13 , further comprising analyzing the complementary DNA molecules using an array-based technology.